Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2207
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14751
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:994 original size:29 final size:30
Alignment explanation
Indices: 935--992 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
925 TCCGAGCCTT
*
935 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
965 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
993 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:1221 original size:13 final size:13
Alignment explanation
Indices: 1203--1234 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1193 TTTCCAGCAA
1203 TTATGAATTTATT
1 TTATGAATTTATT
1216 TTATGAATTTATT
1 TTATGAATTTATT
*
1229 TGATGA
1 TTATGA
1235 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1458 original size:49 final size:50
Alignment explanation
Indices: 1329--1569 Score: 288
Period size: 49 Copynumber: 4.7 Consensus size: 50
1319 ATTTGGGTAA
* * *
1329 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
1385 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1435 AGAGGT-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1484 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
1534 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
1570 TTTGGCATGT
Statistics
Matches: 164, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
49 46 0.28
50 44 0.27
51 29 0.18
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1515 original size:99 final size:104
Alignment explanation
Indices: 1333--1577 Score: 349
Period size: 99 Copynumber: 2.4 Consensus size: 104
1323 GGGTAAAGAG
*
1333 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCCTGT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCCCTAT
* *
1398 AAGACCATGTCTGGGACATGGCATGGGCACCGA-GACGAG-AG
63 AAGACCATGTCTGGGACATGGCATGGGCACC-ATCACGAGAAC
* * *
1439 GT-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTATAAG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTATAAG
1500 ACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
66 ACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
*
1539 ATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1578 GTTATTATCA
Statistics
Matches: 127, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
98 1 0.01
99 51 0.40
100 4 0.03
101 34 0.27
104 2 0.02
105 34 0.27
106 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (104 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTATAAG
ACCATGTCTGGGACATGGCATGGGCACCATCACGAGAAC
Found at i:5778 original size:26 final size:26
Alignment explanation
Indices: 5748--5799 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5738 CACCGCTGAA
*
5748 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
5774 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
5800 CTTTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:6238 original size:29 final size:29
Alignment explanation
Indices: 6205--6268 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
6195 TAATCCACCA
6205 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
6234 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
6264 CCCAA
1 CCCAA
6269 GCTCGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:6242 original size:30 final size:30
Alignment explanation
Indices: 6212--6268 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6202 CCACCCAACT
6212 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
6241 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
6269 GCTCGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:13324 original size:27 final size:27
Alignment explanation
Indices: 13289--13340 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
13279 CCACTGAATC
* *
13289 GGGGAATCATCACTTAGCAACCCCTCG
1 GGGGAATCAGCACATAGCAACCCCTCG
13316 GGGGAATCAGCACATAGCAACCCCT
1 GGGGAATCAGCACATAGCAACCCCT
13341 TTTCATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (27 bp):
GGGGAATCAGCACATAGCAACCCCTCG
Found at i:13412 original size:70 final size:71
Alignment explanation
Indices: 13299--13448 Score: 248
Period size: 70 Copynumber: 2.1 Consensus size: 71
13289 GGGGAATCAT
* *
13299 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTT-TCATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATACAATGG
13363 ATATCG
66 ATATCG
***
13369 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATATGGTGG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATACAATGG
13434 ATATCG
66 ATATCG
13440 CACTTAGCA
1 CACTTAGCA
13449 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 44 0.59
71 30 0.41
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCTTTCACATTTCAAAGATACAATGG
ATATCG
Found at i:13489 original size:25 final size:25
Alignment explanation
Indices: 13461--13509 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
13451 ACCAATGAAC
*
13461 CGGGGAATCAGCACTTAGCAACCCT
1 CGGGGAATCAGCACATAGCAACCCT
13486 CGGGGAATCAGCACATAGCAACCC
1 CGGGGAATCAGCACATAGCAACCC
13510 CCTTTCACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.12
Consensus pattern (25 bp):
CGGGGAATCAGCACATAGCAACCCT
Found at i:13500 original size:101 final size:101
Alignment explanation
Indices: 13368--13585 Score: 343
Period size: 102 Copynumber: 2.1 Consensus size: 101
13358 AATGGATATC
13368 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAA-CCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
*
13432 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
65 GGATCA-CGCACATAGCACCACC-AT-AACCGGGGAATCA
13471 GCACTTAGCAACCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
*
13535 GATCACGCACATAGCACCACCATAATCGGGGAATCA
66 GATCACGCACATAGCACCACCATAACCGGGGAATCA
**
13571 GCACACAGCAACCCT
1 GCACTTAGCAACCCT
13586 TTATATACAA
Statistics
Matches: 109, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
100 25 0.23
101 22 0.20
102 50 0.46
103 12 0.11
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (101 bp):
GCACTTAGCAACCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATCACGCACATAGCACCACCATAACCGGGGAATCA
Found at i:13943 original size:29 final size:29
Alignment explanation
Indices: 13910--13973 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
13900 TAATCCACCA
13910 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
13939 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
13969 CCCAA
1 CCCAA
13974 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:13947 original size:30 final size:30
Alignment explanation
Indices: 13917--13973 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
13907 CCACCCAACT
13917 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
13946 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
13974 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Done.